☰ Navigation Tabs
Crystal Structure of E. coli pseudouridine synthase RluE
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KSV PDB entry 1KSV with the N-terminal domain removed
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 294 4 mg/ml protein in 10 mM Tris, pH 7.5, with 2mM EDTA and 2mM DTT equilibrated against 22% (w/v) MME PEG 2000, 200 mM ammonium sulfate and 100 mM sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 1.97 37.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.015 α = 90 b = 78.887 β = 90 c = 84.182 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 double crystal monochrometer 2003-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.3.1 ALS 8.3.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.6 40 93.2 0.096 14 3.1 49168 -3 -3 15.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.6 1.66 98.4 0.778 2.9 3.3 5102
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1KSV with the N-terminal domain removed 1.6 28.78 45764 45764 2319 86.77 0.215 0.215 0.213 0.215 0.255 0.2573 RANDOM 19.928
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.585 r_dihedral_angle_4_deg 21.079 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_1_deg 5.861 r_scangle_it 4.245 r_scbond_it 2.831 r_mcangle_it 1.954 r_angle_refined_deg 1.457 r_mcbond_it 1.195 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.585 r_dihedral_angle_4_deg 21.079 r_dihedral_angle_3_deg 13.874 r_dihedral_angle_1_deg 5.861 r_scangle_it 4.245 r_scbond_it 2.831 r_mcangle_it 1.954 r_angle_refined_deg 1.457 r_mcbond_it 1.195 r_nbtor_refined 0.311 r_nbd_refined 0.198 r_symmetry_vdw_refined 0.175 r_symmetry_hbond_refined 0.166 r_xyhbond_nbd_refined 0.161 r_chiral_restr 0.095 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2835 Nucleic Acid Atoms Solvent Atoms 281 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction ELVES refinement CNS phasing